Codon degeneracy

DNA consists of a chemically linked sequence of four nucleotides. Each trinucleotide sequence is coded for a corresponding amino acid. Because of the codon degeneracy, some amino acids are coded by more than one triplet. Since a library of random peptides should contain all the possible sequences, the corresponding DNA fragments would have to be degenerated oligonucleotides, which are chemically synthesized as a mixture of sequences. 

In a nonoverlapping code, each individual nucleotide mutation would change at most one amino acid in the protein sequence. (Because of codon degeneracy, some individual mutations vUll not change the amino acid sequence.) In an overlapping code, some mutations (but not all) will change the identity of two consecutive amino acids in the... 

Figure 5.8 A total of 20 amino add residues lining the binding pocket ofYqjM, mainly above the flavin, were addressed by saturation mutagenesis (CAST, single-residue sites with NNK codon degeneracy) [37], Residues with a star did not lead to improved mutants. Cartoon model of YqjM from PDB entry 1Z44 is illustrated (Chain B, white Chain A, green red...

While most protein synthesis occurs in the cytoplasm, mitochondria also have small chromosomes and synthesize some of their own proteins. For example, the human mitochondrial chromosome is composed of less than 17,000 bp and encodes 13 proteins, 22 tRNAs, and 2 rRNAs. Mitochondria use a genetic code that is slightly different from the standard code shown in Table I. Codon degeneracy is greater in mitochondria for example, UGA is not used as a termination signal, but instead codes for tryptophan. Likewise, the trinucleotide AUA codes for methionine (and is also an initiation signal) in mammalian mitochondria, while in the standard code AUA specifies isoleucine. Last, only 22 tRNAs are used to decode all 61 sense codons, in contrast to the 60 or so that are used in prokaryotes or the cytoplasm of eukaryotes. 

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